Amid rumours of plans to repeal Articles 370 and 35A, which allow Jammu a special status and privileges, the governor said in a statement that the state has no knowledge of any changes to constitutional provisions.
Despite the assurance from the Governor, the Congress and the National Conference indicated that they would seek clarifications from the Centre when Parliament meets again on Monday.
Abdullah said the party needed the assurance as the Governor is not the final word on Jammu and Kashmir'.
The advisory asking pilgrims and tourists to leave had cited security concerns.
The Jammu and Kashmir Tourism Department sent buses on Friday, immediately after the advisory was issued, to different tourist destinations to bring the visitors back to Srinagar, Director, Tourism Kashmir, Nissar Wani, said.
The sudden turn of events has left many unhappy, including the business community.
"I have been visiting Kashmir for past so many years, but have never seen such an irresponsible behaviour by the government," Anil Verma, a tourist from Delhi, said.
Haryana's Ramesh Kumar said the government order was "unprecedented".
"We have been coming here for many years, but we have never seen such an advisory from the government, he said.
We were enjoying ourselves, but the order has led to chaos and fear," he said.
Governor Malik told a delegation led by Omar Abdullah that a pure security measure is being mixed up with issues with which it has no connection.
That is the cause of the panic," he said, according to the Raj Bhavan.
"There were credible inputs which were available to the security agencies regarding terrorist attacks on the Amarnath Yatra. There has been intensified shelling on the LoC by Pakistan, which was responded to effectively by the Army," he told the delegation.
But Abdullah said he has asked party MPs to move a motion in Parliament on Monday seeking a statement from the Union government on the situation that has developed in the state over the past few weeks.
The Jammu and Kashmir Pradesh Congress Committee (JKPCC) also expressed concern.
No one knows what is happening. There is uncertainty. We are seeing this type of situation for the first time and it has raised questions. We want the Centre as well as the state government to clarify what is going on," JKPCC president G A Mir told reporters.
He said the deployment of additional forces, orders by different departments and the advisory asking tourists and yatris to leave have created panic.
"All this leads to speculation that something is happening behind the curtain, he added.
Tourism director Wani said about 20,000-22,000 tourists were in Kashmir on Friday.
According to the Airports Authority of India, 6,126 passengers reported at the Srinagar International Airport on Saturday to travel out of the Valley.
Out of this, 5,829 passengers travelled by 32 scheduled flights. The remaining 387 passengers were accommodated in four IAF aircraft and flown to destinations like Jammu, Pathankot and Hindon..
Kashmir Chamber of Commerce and Industry (KCCI) said the government advisory has "in a single fell swoop, caused irreversible damage to the economy of the state."
The advisory was issued after the Army on Friday said Pakistan-based terrorists were planning to target the Amarnath Yatra.
A top Army official said searches in the past few days had led to the recovery of a Pakistan-made mine and a huge cache of arms along the yatra route.
The BJP's Jammu and Kashmir unit on Saturday accused leaders of the NC, the PDP and the Congress of deliberately trying to trigger panic as they themselves are frightened.
"The common man has no fear and under the leadership of Modi, every common citizen is safe in the country," he party's state president Ravinder Raina said in Jammu.
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